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In Print: Last Week's Microarray Papers of Note: Sep 24, 2013


IQCB1 and PDE6B mutations cause similar early onset retinal degenerations in two closely related terrier dog breeds.

Invest Ophthalmol Vis Sci. 2013 Sep 17. [Epub ahead of print]

Goldstein O, et al.

The authors used Illumina and Affymetrix canine SNP genotyping arrays to identify the causative mutations in two early onset canine retinal degenerations, segregating in the American Staffordshire terrier and the Pitt bull terrier breeds.

The evaluation of the usefulness of pedigree verification-dedicated SNPs for breed assignment in three polish cattle populations.

Mol Biol Rep. 2013 Sep 22. [Epub ahead of print]

Gurgul A, et al.

In this study, the authors attempted to determine the breed of origin of 741 cattle by using 120 SNPs dedicated for parentage testing and included in Illumina's BovineSNP50 BeadChip genotyping assay. While the applied Bayesian and frequency-based methods allowed such differentiation, they report that the reliability of the results was "not completely satisfying," and suggest that the studied markers are "not the best tool for breed assignment."

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge.

Bioinformatics. 2013 Sep 20. [Epub ahead of print]

Tarca A, et al.

The authors describe the results of an international collaboration called the IMPROVER Diagnostic Signature Challenge. Fifty-four teams used public data to develop prediction models in four disease areas including multiple sclerosis, lung cancer, psoriasis and chronic obstructive pulmonary disease, and made predictions on blinded new data that was generated. This paper presents the challenge results and introduces to the community the approaches of the best overall three performers, as well as an R package that implements the approach of the best team.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.